9G5E | pdb_00009g5e

Translation-initiation state of human mitochondrial ribosome small subunit (State F)


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
A [auth 0]SCOP2B SuperfamilyTranslation proteins SH3-like KOW motif containing domain 8091481 3000334 SCOP2B (2022-06-29)
H [auth B]SCOP2B SuperfamilySIS domain/Ribosomal protein S2-like 8063850 3001397 SCOP2B (2022-06-29)
O [auth I]SCOP2B SuperfamilyTranslational machinery components 8098948 3000571 SCOP2B (2022-06-29)
P [auth J]SCOP2B SuperfamilyNucleic acid-binding proteins 8095431 3000135 SCOP2B (2022-06-29)
Q [auth K]SCOP2B SuperfamilyGlucocorticoid receptor-like (DNA-binding domain) 8052599 3000068 SCOP2B (2022-06-29)
W [auth Q]SCOP2B SuperfamilyRibosomal protein S21 8053089 3002159 SCOP2B (2022-06-29)
X [auth R]SCOP2B SuperfamilyMitochondrial 28S ribosomal protein S22-like 8051932 3002074 SCOP2B (2022-06-29)
EA [auth Y]SCOP2B SuperfamilyMitochondrial 28S ribosomal protein S31-like 8090914 3002471 SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A [auth 0]PF16053Mitochondrial 28S ribosomal protein S34 (MRP-S34)Mitochondrial 28S ribosomal protein S34- Family
B [auth 1]PF10213Mitochondrial ribosomal subunit protein (MRP-S28)Mitochondrial ribosomal subunit protein- Family
C [auth 2]PF06747CHCH domain (CHCH)CHCH domainwe have identified a conserved motif in the LOC118487 protein that we have called the CHCH motif. Alignment of this protein with related members showed the presence of three subgroups of proteins, which are called the S (Small), N (N-terminal extende ...we have identified a conserved motif in the LOC118487 protein that we have called the CHCH motif. Alignment of this protein with related members showed the presence of three subgroups of proteins, which are called the S (Small), N (N-terminal extended) and C (C-terminal extended) subgroups. All three sub-groups of proteins have in common that they contain a predicted conserved [coiled coil 1]-[helix 1]-[coiled coil 2]-[helix 2] domain (CHCH domain). Within each helix of the CHCH domain, there are two cysteines present in a C-X9-C motif. The N-group contains an additional double helix domain, and each helix contains the C-X9-C motif. This family contains a number of characterised proteins: Cox19 protein - a nuclear gene of Saccharomyces cerevisiae, codes for an 11-kDa protein (Cox19p) required for expression of cytochrome oxidase. Because cox19 mutants are able to synthesise the mitochondrial and nuclear gene products of cytochrome oxidase, Cox19p probably functions post-translationally during assembly of the enzyme. Cox19p is present in the cytoplasm and mitochondria, where it exists as a soluble intermembrane protein. This dual location is similar to what was previously reported for Cox17p, a low molecular weight copper protein thought to be required for maturation of the CuA centre of subunit 2 of cytochrome oxidase. Cox19p have four conserved potential metal ligands, these are three cysteines and one histidine. Mrp10 - belongs to the class of yeast mitochondrial ribosomal proteins that are essential for translation [2]. Eukaryotic NADH-ubiquinone oxidoreductase 19 kDa (NDUFA8) subunit [3]. The CHCH domain was previously called DUF657 [4].
Domain
E [auth 4]PF13812Pentatricopeptide repeat domain (PPR_3)Pentatricopeptide repeat domain- Repeat
E [auth 4]PF22330Small ribosomal subunit protein mS39, PPR (Rib_mS39_PPR)Small ribosomal subunit protein mS39, PPR- Repeat
F [auth 7]PF00009Elongation factor Tu GTP binding domain (GTP_EFTU)Elongation factor Tu GTP binding domainThis domain contains a P-loop motif, also found in several other families such as Pfam:PF00071, Pfam:PF00025 and Pfam:PF00063. Elongation factor Tu consists of three structural domains, this plus two C-terminal beta barrel domains. Domain
F [auth 7]PF22042Elongation factor G domain 2 (EF-G_D2)Elongation factor G domain 2Elongation factor G (EF-G) catalyzes the translocation step of translation. It consists of five structural domains, this entry represents the second domain [1]. This domain adopts a beta barrel structure. This family also includes domains found in ot ...Elongation factor G (EF-G) catalyzes the translocation step of translation. It consists of five structural domains, this entry represents the second domain [1]. This domain adopts a beta barrel structure. This family also includes domains found in other translation factors such as translation initiation factor IF-2, peptide chain release factor, etc.
Domain
H [auth B]PF00318Ribosomal protein S2 (Ribosomal_S2)Ribosomal protein S2- Family
I [auth C]PF14955Mitochondrial ribosome subunit S24 (MRP-S24)Mitochondrial ribosome subunit S24- Family
J [auth D]PF03719Ribosomal protein S5, C-terminal domain (Ribosomal_S5_C)Ribosomal protein S5, C-terminal domainDomain
J [auth D]PF21251Small ribosomal subunit protein uS5m, N-terminal (Ribosomal_uS5m_N)Small ribosomal subunit protein uS5m, N-terminalThis entry represents an extension found at the N-terminal of the mitochondrial 28S Small ribosomal subunit protein uS5m [1,2]. This region lines a part of the mRNA entry path and connects the 28S subunit body to the head forming a latch across the m ...This entry represents an extension found at the N-terminal of the mitochondrial 28S Small ribosomal subunit protein uS5m [1,2]. This region lines a part of the mRNA entry path and connects the 28S subunit body to the head forming a latch across the mRNA channel entrance [2].
Domain
J [auth D]PF00333Ribosomal protein S5, N-terminal domain (Ribosomal_S5)Ribosomal protein S5, N-terminal domainDomain
K [auth E]PF01250Ribosomal protein S6 (Ribosomal_S6)Ribosomal protein S6Domain
L [auth F]PF00177Ribosomal protein S7p/S5e (Ribosomal_S7)Ribosomal protein S7p/S5eThis family contains ribosomal protein S7 from prokaryotes and S5 from eukaryotes. Domain
M [auth G]PF00380Ribosomal protein S9/S16 (Ribosomal_S9)Ribosomal protein S9/S16- Family
N [auth H]PF00338Ribosomal protein S10p/S20e (Ribosomal_S10)Ribosomal protein S10p/S20eThis family includes small ribosomal subunit S10 from prokaryotes and S20 from eukaryotes. Domain
O [auth I]PF00411Ribosomal protein S11 (Ribosomal_S11)Ribosomal protein S11- Family
P [auth J]PF00164Ribosomal protein S12/S23 (Ribosom_S12_S23)Ribosomal protein S12/S23This protein is known as S12 in bacteria and archaea and S23 in eukaryotes. Domain
Q [auth K]PF00253Ribosomal protein S14p/S29e (Ribosomal_S14)Ribosomal protein S14p/S29e- Family
R [auth L]PF00312Ribosomal protein S15 (Ribosomal_S15)Ribosomal protein S15Domain
S [auth M]PF00886Ribosomal protein S16 (Ribosomal_S16)Ribosomal protein S16- Family
T [auth N]PF00366Ribosomal protein S17 (Ribosomal_S17)Ribosomal protein S17Domain
U [auth O]PF01084Ribosomal protein S18 (Ribosomal_S18)Ribosomal protein S18- Family
V [auth P]PF01084Ribosomal protein S18 (Ribosomal_S18)Ribosomal protein S18- Family
W [auth Q]PF01165Ribosomal protein S21 (Ribosomal_S21)Ribosomal protein S21- Family
X [auth R]PF10245Mitochondrial 28S ribosomal protein S22 (MRP-S22)Mitochondrial 28S ribosomal protein S22- Family
Y [auth S]PF10484Mitochondrial ribosomal protein S23 (MRP-S23)Mitochondrial ribosomal protein S23- Family
Z [auth T]PF05047Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain (L51_S25_CI-B8)Mitochondrial ribosomal protein L51 / S25 / CI-B8 domainThe proteins in this family are located in the mitochondrion. The family includes ribosomal protein L51, and S25. This family also includes mitochondrial NADH-ubiquinone oxidoreductase B8 subunit (CI-B8) EC:1.6.5.3. It is not known whether all member ...The proteins in this family are located in the mitochondrion. The family includes ribosomal protein L51, and S25. This family also includes mitochondrial NADH-ubiquinone oxidoreductase B8 subunit (CI-B8) EC:1.6.5.3. It is not known whether all members of this family form part of the NADH-ubiquinone oxidoreductase and whether they are also all ribosomal proteins. Structurally related to thioredoxin-fold.
Domain
AA [auth U]PF14943Mitochondrial ribosome subunit S26 (MRP-S26)Mitochondrial ribosome subunit S26- Family
DA [auth X]PF10236Mitochondrial ribosomal death-associated protein 3 (DAP3)Mitochondrial ribosomal death-associated protein 3- Family
FA [auth Z]PF08293Mitochondrial ribosomal subunit S27 (MRP-S33)Mitochondrial ribosomal subunit S27- Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A [auth 0]28S ribosomal protein S34, mitochondrial
B [auth 1]28S ribosomal protein S35, mitochondrial
C [auth 2]Small ribosomal subunit protein mS37
D [auth 3]Aurora kinase A-interacting protein-
E [auth 4]Pentatricopeptide repeat domain-containing protein 3, mitochondrial
F [auth 7]Translation initiation factor IF-2, mitochondrial
G [auth A]12S mitochondrial rRNA---
H [auth B]28S ribosomal protein S2, mitochondrial
I [auth C]28S ribosomal protein S24, mitochondrial
J [auth D]28S ribosomal protein S5, mitochondrial
K [auth E]28S ribosomal protein S6, mitochondrial
L [auth F]28S ribosomal protein S7, mitochondrial
M [auth G]28S ribosomal protein S9, mitochondrial
N [auth H]28S ribosomal protein S10, mitochondrial-
O [auth I]28S ribosomal protein S11, mitochondrial
P [auth J]28S ribosomal protein S12, mitochondrial
Q [auth K]28S ribosomal protein S14, mitochondrial
R [auth L]28S ribosomal protein S15, mitochondrial
S [auth M]28S ribosomal protein S16, mitochondrial
T [auth N]28S ribosomal protein S17, mitochondrial
U [auth O]28S ribosomal protein S18b, mitochondrial
V [auth P]28S ribosomal protein S18c, mitochondrial
W [auth Q]28S ribosomal protein S21, mitochondrial
X [auth R]28S ribosomal protein S22, mitochondrial
Y [auth S]28S ribosomal protein S23, mitochondrial
Z [auth T]28S ribosomal protein S25, mitochondrial
AA [auth U]28S ribosomal protein S26, mitochondrial
BA [auth V]28S ribosomal protein S27, mitochondrial
CA [auth W]28S ribosomal protein S28, mitochondrial
DA [auth X]28S ribosomal protein S29, mitochondrial
EA [auth Y]28S ribosomal protein S31, mitochondrial
FA [auth Z]28S ribosomal protein S33, mitochondrial

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
A [auth 0]IPR032053Small ribosomal subunit protein mS34Family
B [auth 1]IPR039848Small ribosomal subunit protein mS35, mitochondrialFamily
B [auth 1]IPR019349Small ribosomal subunit protein mS35, mitochondrial, conserved domainDomain
C [auth 2]IPR010625CHCHDomain
C [auth 2]IPR009069Cysteine alpha-hairpin motif superfamilyHomologous Superfamily
C [auth 2]IPR033620Small ribosomal subunit protein mS37, metazoanFamily
D [auth 3]IPR013177Ribosomal protein mS38, C-terminalDomain
E [auth 4]IPR037387Pentatricopeptide repeat domain-containing protein 3Family
E [auth 4]IPR011990Tetratricopeptide-like helical domain superfamilyHomologous Superfamily
E [auth 4]IPR002885Pentatricopeptide repeatRepeat
E [auth 4]IPR055063Small ribosomal subunit protein mS39, PPRRepeat
F [auth 7]IPR005225Small GTP-binding domainDomain
F [auth 7]IPR000178Translation initiation factor IF-2, bacterial-likeFamily
F [auth 7]IPR000795Translational (tr)-type GTP-binding domainDomain
F [auth 7]IPR053905Elongation factor G-like, domain IIDomain
F [auth 7]IPR044145Translation initiation factor IF-2, domain IIDomain
F [auth 7]IPR009000Translation protein, beta-barrel domain superfamilyHomologous Superfamily
F [auth 7]IPR015760Translation initiation factor IF- 2Family
F [auth 7]IPR036925Translation initiation factor IF-2, domain 3 superfamilyHomologous Superfamily
F [auth 7]IPR023115Translation initiation factor IF- 2, domain 3Domain
F [auth 7]IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
H [auth B]IPR005706Small ribosomal subunit protein uS2, bacteria/mitochondria/plastidFamily
H [auth B]IPR023591Small ribosomal subunit protein uS2, flavodoxin-like domain superfamilyHomologous Superfamily
H [auth B]IPR018130Small ribosomal subunit protein uS2, conserved siteConserved Site
H [auth B]IPR001865Small ribosomal subunit protein uS2Family
I [auth C]IPR026146Small ribosomal subunit protein uS3m, metazoanFamily
J [auth D]IPR000851Small ribosomal subunit protein uS5Family
J [auth D]IPR048584Small ribosomal subunit protein uS5m, N-terminal domainDomain
J [auth D]IPR005324Small ribosomal subunit protein uS5, C-terminalDomain
J [auth D]IPR013810Small ribosomal subunit protein uS5, N-terminalDomain
J [auth D]IPR020568Ribosomal protein uS5 domain 2-type superfamilyHomologous Superfamily
J [auth D]IPR018192Small ribosomal subunit protein uS5, N-terminal, conserved siteConserved Site
J [auth D]IPR014721Small ribosomal subunit protein uS5 domain 2-type fold, subgroupHomologous Superfamily
K [auth E]IPR000529Small ribosomal subunit protein bS6Family
K [auth E]IPR035980Small ribosomal subunit protein bS6 superfamilyHomologous Superfamily
K [auth E]IPR014717Translation elongation factor EF1B/small ribosomal subunit protein bS6Homologous Superfamily
L [auth F]IPR036823Small ribosomal subunit protein uS7 domain superfamilyHomologous Superfamily
L [auth F]IPR000235Small ribosomal subunit protein uS7Family
L [auth F]IPR023798Small ribosomal subunit protein uS7 domainDomain
M [auth G]IPR020574Small ribosomal subunit protein uS9, conserved siteConserved Site
M [auth G]IPR023035Small ribosomal subunit protein uS9, bacterial/plastidFamily
M [auth G]IPR020568Ribosomal protein uS5 domain 2-type superfamilyHomologous Superfamily
M [auth G]IPR000754Small ribosomal subunit protein uS9Family
M [auth G]IPR014721Small ribosomal subunit protein uS5 domain 2-type fold, subgroupHomologous Superfamily
N [auth H]IPR027486Small ribosomal subunit protein uS10 domainDomain
N [auth H]IPR040055Small ribosomal subunit protein uS10mFamily
N [auth H]IPR036838Small ribosomal subunit protein uS10 domain superfamilyHomologous Superfamily
O [auth I]IPR001971Small ribosomal subunit protein uS11Family
O [auth I]IPR036967Small ribosomal subunit protein uS11 superfamilyHomologous Superfamily
O [auth I]IPR018102Small ribosomal subunit protein uS11, conserved siteConserved Site
P [auth J]IPR006032Small ribosomal subunit protein uS12Family
P [auth J]IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
P [auth J]IPR005679Ribosomal protein uS12, bacterial-typeFamily
Q [auth K]IPR001209Small ribosomal subunit protein uS14Family
R [auth L]IPR009068uS15/NS1, RNA-binding domain superfamilyHomologous Superfamily
R [auth L]IPR000589Small ribosomal subunit protein uS15Family
R [auth L]IPR005290Small ribosomal subunit protein uS15, bacterial-typeFamily
R [auth L]IPR052137Universal small ribosomal subunit uS15Family
S [auth M]IPR023803Small ribosomal subunit protein bS16 domain superfamilyHomologous Superfamily
S [auth M]IPR000307Small ribosomal subunit protein bS16Family
T [auth N]IPR039193Small ribosomal subunit protein uS17m, metazoaFamily
T [auth N]IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
T [auth N]IPR000266Small ribosomal subunit protein uS17Family
U [auth O]IPR040054Small ribosomal subunit protein mS40Family
U [auth O]IPR001648Small ribosomal subunit protein bS18Family
U [auth O]IPR036870Small ribosomal subunit protein bS18 superfamilyHomologous Superfamily
V [auth P]IPR001648Small ribosomal subunit protein bS18Family
V [auth P]IPR018275Small ribosomal subunit protein bS18, conserved siteConserved Site
V [auth P]IPR036870Small ribosomal subunit protein bS18 superfamilyHomologous Superfamily
W [auth Q]IPR038380Small ribosomal subunit protein bS21 superfamilyHomologous Superfamily
W [auth Q]IPR001911Small ribosomal subunit protein bS21Family
X [auth R]IPR019374Small ribosomal subunit protein mS22Family
Y [auth S]IPR023611Small ribosomal subunit protein mS23, conserved domainDomain
Y [auth S]IPR019520Small ribosomal subunit protein mS23, metazoaFamily
Z [auth T]IPR007741Ribosomal protein/NADH dehydrogenase domainDomain
Z [auth T]IPR036249Thioredoxin-like superfamilyHomologous Superfamily
Z [auth T]IPR040049Ribosomal subunit protein mS25/mL61, mitochondrialFamily
AA [auth U]IPR026140Small ribosomal subunit protein mS26Family
BA [auth V]IPR011990Tetratricopeptide-like helical domain superfamilyHomologous Superfamily
BA [auth V]IPR002885Pentatricopeptide repeatRepeat
BA [auth V]IPR019266Small ribosomal subunit protein mS27Family
BA [auth V]IPR034913mS27/PTCD2Family
CA [auth W]IPR019375Small ribosomal subunit protein bS1mFamily
DA [auth X]IPR008092Small ribosomal subunit protein mS29, metazoan-typeFamily
DA [auth X]IPR019368Small ribosomal subunit protein mS29Family
DA [auth X]IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
EA [auth Y]IPR026299Mitochondrial 28S ribosomal protein S31Family
FA [auth Z]IPR013219Small ribosomal subunit protein mS33Family

Pharos: Disease Associations Pharos Homepage Annotation

ChainsDrug Target  Associated Disease
A [auth 0]PharosP82930
B [auth 1]PharosP82673
C [auth 2]PharosQ96BP2
D [auth 3]PharosQ9NWT8
E [auth 4]PharosQ96EY7
F [auth 7]PharosP46199
H [auth B]PharosQ9Y399
J [auth D]PharosP82675
K [auth E]PharosP82932
L [auth F]PharosQ9Y2R9
M [auth G]PharosP82933
N [auth H]PharosP82664
O [auth I]PharosP82912
P [auth J]PharosO15235
Q [auth K]PharosO60783
R [auth L]PharosP82914
S [auth M]PharosQ9Y3D3
T [auth N]PharosQ9Y2R5
U [auth O]PharosQ9Y676
V [auth P]PharosQ9Y3D5
W [auth Q]PharosP82921
X [auth R]PharosP82650
Y [auth S]PharosQ9Y3D9
Z [auth T]PharosP82663
BA [auth V]PharosQ92552
CA [auth W]PharosQ9Y2Q9
DA [auth X]PharosP51398
EA [auth Y]PharosQ92665
FA [auth Z]PharosQ9Y291

Protein Modification Annotation

Modified Residue(s)
ChainResidue(s)Description
C [auth 2]ACE RESIDAA0041 , AA0042 , AA0043 , AA0044 , AA0045 , AA0046 , AA0049 , AA0050 , AA0051 , AA0052 , AA0053 , AA0054 , AA0354

PSI-MOD :  N-acetyl-L-alanine MOD:00050 , N-acetyl-L-aspartic acid MOD:00051 , N-acetyl-L-cysteine MOD:00052 , N-acetyl-S-archeol-cysteine MOD:00897 , N-acetyl-L-glutamic acid MOD:00053 , N-acetyl-L-glutamine MOD:00054 , N-acetylglycine MOD:00055 , N-acetyl-L-methionine MOD:00058 , N-acetyl-L-proline MOD:00059 , N-acetyl-L-serine MOD:00060 , N,O-diacetylated L-serine MOD:00648 , N-acetyl-L-threonine MOD:00061 , N-acetyl-L-tyrosine MOD:00062 , N-acetyl-L-valine MOD:00063 , N2-acetyl-L-arginine MOD:00359